| 1. |
- Agostinelli, Marta, et al.
(författare)
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Pedunculate Oaks (Quercus robur L.) Differing in Vitality as Reservoirs for Fungal Biodiversity
- 2018
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Ecological significance of trees growing in urban and peri-urban settings is likely to increase in future land-use regimes, calling for better understanding of their role as potential reservoirs or stepping stones for associated biodiversity. We studied the diversity of fungal endophytes in woody tissues of asymptomatic even aged pedunculate oak trees, growing as amenity trees in a peri-urban setting. The trees were classified into three groups according to their phenotypic vitality (high, medium, and low). Endophytes were cultured on potato dextrose media from surface sterilized twigs and DNA sequencing was performed to reveal the taxonomic identity of the morphotypes. In xylem tissues, the frequency and diversity of endophytes was highest in oak trees showing reduced vitality. This difference was not found for bark samples, in which the endophyte infections were more frequent and communities more diverse than in xylem. In general, most taxa were shared across the samples with few morphotypes being recovered in unique samples. Leaf phenolic profiles were found to accurately classify the trees according to their phenotypic vitality. Our results confirm that xylem is more selective substrate for endophytes than bark and that endophyte assemblages in xylem are correlated to the degree of host vitality. Thus, high vitality of trees may be associated with reduced habitat quality to wood-associated endophytes.
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| 2. |
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| 3. |
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| 4. |
- Cleary, Michelle
(författare)
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Cryptic Risks to Forest Biosecurity Associated with the Global Movement of Commercial Seed
- 2019
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Ingår i: Forests. - : MDPI AG. - 1999-4907. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- The import and export of tree seed carries with it risks of inadvertent introduction of pests and pathogens to hitherto unaffected regions. Although trade in seed of specified trees is regulated, phytosanitary requirements for most tree species are minimal, even those related to the most important forest tree species in a given region. A better understanding of the microbiome associated with seed intended for commercial production or ornamental use, and their potential risk with the transport from the source origin of distributors, will help regulatory agencies implement measures to safeguard seed health and avoid trade-related spread of potentially harmful pathogens. In this study we used high-throughput sequencing to show that highly diverse fungal communities were associated with seed of 14 different Pinus species obtained from seed banks (seed orchards) and retail sources (online distributors) in North America and Europe. Fungal diversity differed among the 23 seedlots tested. Community composition did not relate to the species of Pinus nor the country of origin. Assigned potential functions based on sequence identity using FUNGuild provided an overall understanding of the likely life strategies of fungal operational taxonomic units (OTUs). Of those sequences classified to a trophic level, 453 were plant pathogens, with the Dothideomycetes having the highest prevalence. The most common plant pathogens included Sydowia polyspora, Lasiodiplodia theobromae, Diplodia intermedia and Diplodia sapinea that were detected from the majority of Pinus species. The evidence presented here illustrates an urgent need for plant protection authorities, practitioners and the general public to recognize the potential risk of introducing harmful pathogens through innocent transport of seed.
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| 5. |
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| 6. |
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| 7. |
- Cleary, Michelle
(författare)
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Effects of Host Variability on the Spread of Invasive Forest Diseases
- 2017
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Ingår i: Forests. - : MDPI AG. - 1999-4907. ; 8
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Forskningsöversikt (refereegranskat)abstract
- Biological invasions, resulting from deliberate and unintentional species transfers of insects, fungal and oomycete organisms, are a major consequence of globalization and pose a significant threat to biodiversity. Limiting damage by non-indigenous forest pathogens requires an understanding of their current and potential distributions, factors affecting disease spread, and development of appropriate management measures. In this review, we synthesize innate characteristics of invading organisms (notably mating system, reproduction type, and dispersal mechanisms) and key factors of the host population (namely host diversity, host connectivity, and host susceptibility) that govern spread and impact of invasive forest pathogens at various scales post-introduction and establishment. We examine spread dynamics for well-known invasive forest pathogens, Hymenoscyphus fraxineus (T. Kowalski) Baral, Queloz, Hosoya, comb. nov., causing ash dieback in Europe, and Cryphonectria parasitica, (Murr.) Barr, causing chestnut blight in both North America and Europe, illustrating the importance of host variability (diversity, connectivity, susceptibility) in their invasion success. While alien pathogen entry has proven difficult to control, and new biological introductions are indeed inevitable, elucidating the key processes underlying host variability is crucial for scientists and managers aimed at developing effective strategies to prevent future movement of organisms and preserve intact ecosystems.
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| 8. |
- Cleary, Michelle
(författare)
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First report of Lecanosticta acicola on non-native Pinus mugo in southern Sweden
- 2019
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Ingår i: Forest Pathology. - : Wiley. - 1437-4781 .- 1439-0329. ; 49
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Tidskriftsartikel (refereegranskat)abstract
- In 2017, severe symptoms of brown spot needle blight, similar to those caused by Lecanosticta acicola, were observed on needles of non-native Pinus mugo var. Hesse planted in an arboretum in southern Sweden. Microscopic characterization and molecular diagnostics of isolates obtained from diseased needles confirmed the identity of L. acicola. This is the first report of the quarantine pathogen L. acicola in Sweden. Subsequent surveys are urgently needed to assess the presence and extent of the L. acicola invasion in Scots pine (Pinus sylvestris) stands in Sweden and other Scandinavian countries.
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| 9. |
- Cleary, Michelle, et al.
(författare)
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First Report of Phytophthora gonapodyides Causing Stem Canker on European Beech (Fagus sylvatica) in Southern Sweden
- 2016
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Ingår i: Plant Disease. - 0191-2917 .- 1943-7692. ; 100, s. 2174-2175
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Tidskriftsartikel (refereegranskat)abstract
- Since 2010, extensive crown transparency of European beech (Fagus sylvatica) has been recorded in southern Sweden, with Phytophthora cambivora, P. plurivora, and P. cactorum as well as associated climatic triggers believed to be the major factors involved. In 2015, a different Phytophthora sp. was isolated from three F. sylvatica trees showing characteristic bleeding canker symptoms in Pildammsparken in Malmö, Sweden. Small sections of inner phloem were dissected at the interface between necrotic and healthy tissue, directly plated onto PAR(PH)-V8 selective medium containing 0.250 g/liter sodium ampicillin, 0.01 g/liter benomyl, 0.05 g/liter hymexazol, 0.1 g/liter PCNB, 0.05 g/liter pimaricin, and 0.01 g/liter rifamycin, and incubated at 20°C in darkness. Growing hyphae were later transferred to PDA and incubated at 20°C in the dark. The colony pattern was stellate. The average radial growth rate at 20°C was 0.6 cm/day. These morphological features are similar to that previously described for P. gonapodyides (Corcobado et al. 2010; Erwin and Ribeiro 1996; Jung et al. 1996). The isolates grown on PDA formed irregularly branched hyphae. Nonpapillate, elongated-ovoid to obpyriform sporangia (∼50 × 40 µm) were produced after 7 days by incubating on V8 agar culture (nonsterile soil water). DNA was extracted from mycelia and the identity of P. gonapodyides was confirmed by sequencing the internal transcribed (ITS) spacer region of the rDNA with the primers ITS4/ITS6 (GenBank accession nos. KX055998, KX055999, and KX056000). BLAST search showed 99 to 100% identity with reference sequences of P. gonapodyides deposited in GenBank. Pathogenicity on F. sylvatica was confirmed in a greenhouse experiment using two different isolates of P. gonapodyides. Mycelial plugs of 3-week-old cultures of each isolate grown on PDA were inoculated on the stems of 1-year-old seedlings at two locations, separated by 20 cm, by aseptically excising a small 5-mm flap of bark, inserting the mycelial plug along the cambium, and adding a droplet of Milliq H2O before sealing the wound with Parafilm. Ten seedlings were inoculated for each isolate. Controls consisted of stem-wound inoculation with a sterile plug of PDA, and no wounding at all. After 7 weeks, lesion length was measured. All seedlings inoculated with P. gonapodyides showed distinct necrotic lesions, whereas control treatments did not show any symptoms of disease. The average cumulative lesion length on seedlings inoculated with P. gonapodyides was significantly higher than on the wounded control treatment (25.4 mm ± 1.66 vs. 0.4 mm ± 0.01; P < 0.0001 for isolate 1 and 28.9 mm ± 1.42 vs. 0.4 mm ± 0.01; P < 0.001 for isolate 2). Koch's postulates were fulfilled by successfully reisolating the pathogen from infected seedlings. To our knowledge, this is the first report of P. gonapodyides causing disease on trees in Sweden. P. gonapodyides has been noted previously in Denmark (Erwin and Ribeiro 1996), and has been traditionally regarded as a weak parasite with saprophytic abilities, usually associated with aquatic environments such as rivers, riparian areas, and wetlands (Brasier et al. 2003). We cannot exclude that recent climatic triggers such as high summer precipitation coupled with mild winter temperatures have favored conditions to multicyclic spread of P. gonapodyides via zoospores, or that increased average age of beech stands has contributed to their higher susceptibility to weaker pathogens. Damage caused by P. gonapodyides however might be underestimated as it also can inhibit seed germination and is known to cause root rot and stem lesions in Quercus robur and Q. ilex (Corcobado et al. 2010; Jung et al. 1996). The newly reported damage caused by P. gonapodyides on F. sylvatica trees in southern Sweden is alarming particularly since beech is a dominant and ecologically important hardwood species that is widely used in forestry and as a planted ornamental in urban and landscape settings. Furthermore, other hosts such as Alnus glutinosa, Q. petraea, Q. robur (Jung et al. 1996), Picea abies, Betula spp., Acer spp., Tilia spp. (Jung et al. 2009), and Salix spp. (Brasier et al. 2003), also common in southern Sweden, may face an increased risk of damages caused by P. gonapodyides in the future.
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| 10. |
- Cleary, Michelle, et al.
(författare)
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First report of Pleuroceras pseudoplatani on Acer rubrum, A. griseum, A. saccharinurn, A. negundo, A. circinatum and A. macrophyllum in Scotland
- 2018
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Ingår i: Forestry Chronicle. - : Canadian Institute of Forestry. - 0015-7546 .- 1499-9315. ; 94, s. 147-150
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Tidskriftsartikel (refereegranskat)abstract
- In September 2016, large necrotic lesions were observed on the foliage of several maples in Aberdeenshire, Scotland. Symptoms resembled giant leaf blotch disease caused by Pleuroceras pseudoplatani (formerly Gnomonia pseudoplatani; Ophiognomia pseudoplatani) on sycamore maple (Acer pseudoplatanus), a common disease in Europe. Other than A. pseudoplatanus, no other Acer species have previously been reported as hosts for this pathogen. Symptomatic leaves were collected from Acer rubrum, A. rubrum var. Somerset, A. griseum, A. saccharinum, A. negundo, A. macrophyllum, and A. circinatum, and the known host of P pseudoplatani, A. pseudoplatanus. Next generation sequencing was used to determine presence of the suspected P. pseudoplatani and other associated fungi in symptomatic leaves. P pseudoplatani was predominant in all symptomatic samples with 99-100% identity with reference ITS sequences of P pseudoplatani deposited in GenBank (NCBI). This is the first report of P. pseudoplatani associated with leaf blotch on Acer species other than A. pseudoplatanus. The newly reported damage on North American Acer species may be of particular concern because of the economic importance of maples for timber products, syrup production and as ornamental trees in urban landscapes. Precautions should be taken to limit trade of plants from infested areas in Europe.
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| 11. |
- Cleary, Michelle, et al.
(författare)
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Friend or foe? Biological and ecological traits of the European ash dieback pathogen Hymenoscyphus fraxineus in its native environment
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Hymenoscyphus fraxineus, an introduced ascomycete fungus and primary causal agent of European ash dieback, was investigated on Fraxinus mandshurica trees in its native range in Primorye region of Far East Russia. This evidence is the first report of H. fraxineus on healthy, asymptomatic F. mandshurica trees. High-throughput sequencing revealed 49 distinct fungal taxa associated with leaves of F. mandshurica, 12 of which were identified to species level. Phyllosphere fungal assemblages were similar among sites despite being largely geographically distant. Many organisms comprising the foliar fungal community on F. mandshurica in Far East Russia have similarity to those reported inhabiting F. excelsior in Europe based on previous studies. However, Mycosphaerella sp., the most dominant species in this study and detected in nearly all samples, was associated only with F. mandshurica. Genetic diversity of H. fraxineus was significantly higher in the Far East Russian population than in Europe. In contrast to its aggressive behaviour on Fraxinus excelsior in Europe, H. fraxineus appears to be a benign associate of indigenous F. mandshurica that initially induces quiescent and asymptomatic infections in healthy trees prior to active host colonization normally associated with modification of host tissue during senescence.
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| 12. |
- Cleary, Michelle
(författare)
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High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations
- 2019
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 19, s. 47-76
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Forskningsöversikt (refereegranskat)abstract
- High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: (a) to provide a comprehensive overview about the state-of-the-art high-throughput quantification and molecular identification methods used to address population dynamics, community ecology and host associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; (b) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and (c) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Finally, we evaluate the overall perspectives of the state-of-the-art and still evolving methods for diagnostics and population- and community-level ecological research of pathogens and pests.
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| 13. |
- Cleary, Michelle, et al.
(författare)
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Increasing understanding of alien species through citizen science (Alien-CSI)
- 2018
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Ingår i: Research Ideas and Outcomes. - : Pensoft Publishers. - 2367-7163. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- There is no sign of saturation in accumulation of alien species (AS) introductions worldwide, additionally the rate of spread for some species has also been shown to be increasing. However, the challenges of gathering information on AS are recognized. Recent developments in citizen science (CS) provide an opportunity to improve data flow and knowledge on AS while ensuring effective and high quality societal engagement with the issue of IAS (Invasive Alien Species). Advances in technology, particularly on-line recording and smartphone apps, along with the development of social media, have revolutionized CS and increased connectivity while new and innovative analysis techniques are emerging to ensure appropriate management, visualization, interpretation and use and sharing of the data. In early July 2018 we launched a European CO-operation in Science and Technology (COST) Action to address multidisciplinary research questions in relation to developing and implementing CS, advancing scientific understanding of AS dynamics while informing decision-making specifically implementation of technical requirements of relevant legislation such as the EU Regulation 1143/2014 on IAS. It will also support the EU biodiversity goals and embedding science within society. The Action will explore and document approaches to establishing a European-wide CS AS network. It will embrace relevant innovations for data gathering and reporting to support the implementation of monitoring and surveillance measures, while ensuring benefits for society and citizens, through an AS CS European network. The Action will, therefore, increase levels of participation and quality of engagement with current CS initiatives, ensuring and evaluating educational value, and improve the value outcomes for potential users including citizens, scientists, alien species managers, policy-makers, local authorities, industry and other stakeholders.
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| 14. |
- Cleary, Michelle
(författare)
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Insights into the phylogeny of Northern Hemisphere Armillaria: Neighbor-net and Bayesian analyses of translation elongation factor 1-alpha gene sequences
- 2017
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Ingår i: Mycologia. - : Informa UK Limited. - 0027-5514 .- 1557-2536. ; 109, s. 75-91
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Tidskriftsartikel (refereegranskat)abstract
- Armillaria possesses several intriguing characteristics that have inspired wide interest in understanding phylogenetic relationships within and among species of this genus. Nuclear ribosomal DNA sequence based analyses of Armillaria provide only limited information for phylogenetic studies among widely divergent taxa. More recent studies have shown that translation elongation factor 1-alpha (tefl) sequences are highly informative for phylogenetic analysis of Armillaria species within diverse global regions. This study used Neighbor-net and coalescence-based Bayesian analyses to examine phylogenetic relationships of newly determined and existing tefl sequences derived from diverse Armillaria species from across the Northern Hemisphere, with Southern Hemisphere Armillaria species included for reference. Based on the Bayesian analysis of tefl sequences, Armillaria species from the Northern Hemisphere are generally contained within the following four superclades, which are named according to the specific epithet of the most frequently cited species within the superclade: (i) Socialis/Tabescens (exannulate) superclade including Eurasian A. ectypa, North American A. socialis (A. tabescens), and Eurasian A. socialis (A. tabescens) clades; (ii) Mellea superclade including undescribed annulate North American Armillaria sp. (Mexico) and four separate clades of A. mellea (Europe and Iran, eastern Asia, and two groups from North America); (iii) Gallica superclade including Armillaria Nag E (Japan), multiple clades of A. gallica (Asia and Europe), A. calvescens (eastern North America), A. cepistipes (North America), A. altimontana (western USA), A. nabsnona (North America and Japan), and at least two A. gallica clades (North America); and (iv) Solidipes/Ostoyae superclade including two A. solidipes/ostoyae clades (North America), A. gemina (eastern USA), A. solidipes/ostoyae (Eurasia), A. cepistipes (Europe and Japan), A. sinapina (North America and Japan), and A. borealis (Eurasia) Glade 2. Of note is that A. borealis (Eurasia) Glade 1 appears basal to the Solidipes/Ostoyae and Gallica superclades. The Neighbor-net analysis showed similar phylogenetic relationships. This study further demonstrates the utility of tefl for global phylogenetic studies of Armillaria species and provides critical insights into multiple taxonomic issues that warrant further study.
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| 15. |
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| 16. |
- Cleary, Michelle, et al.
(författare)
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Pine Pitch Canker and Insects: Regional Risks, Environmental Regulation, and Practical Management Options
- 2019
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Ingår i: Forests. - : MDPI AG. - 1999-4907. ; 10
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Forskningsöversikt (refereegranskat)abstract
- Pine pitch canker (PPC), caused by the pathogenic fungus Fusarium circinatum (Nirenberg and O' Donnell), is a serious threat to pine forests globally. The recent introduction of the pathogen to Southern Europe and its spread in Mediterranean region is alarming considering the immense ecological and economic importance of pines in the region. Pines in forests and nurseries can be infected, resulting in severe growth losses and mortality. The pathogen is known to spread in plants for planting and in seeds, and results from recent studies have indicated that F. circinatum may also spread through phoretic associations with certain insects. With this review, we aim to expand the current understanding of the risk of insect-mediated spread of PPC in different parts of Europe. Through the joint action of a multinational researcher team, we collate the existing information about the insect species spectrum in different biogeographic conditions and scrutinize the potential of these insects to transmit F. circinatum spores in forests and nurseries. We also discuss the impact of environmental factors and forest management in this context. We present evidence for the existence of a high diversity of insects with potential to weaken pines and disseminate PPC in Europe, including several common beetle species. In many parts of Europe, temperatures are projected to rise, which may promote the activity of several insect species, supporting multivoltinism and thus, further amplifying the risk of insect-mediated dissemination of PPC. Integrated pest management (IPM) solutions that comply with forest management practices need to be developed to reduce this risk. We recommend careful monitoring of insect populations as the basis for successful IPM. Improved understanding of environmental control of the interaction between insects, the pathogen, and host trees is needed in order to support development of bio-rational strategies to safeguard European pine trees and forests against F. circinatum in future.
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| 17. |
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| 18. |
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| 19. |
- Cleary, Michelle, et al.
(författare)
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Sampling and Detection Strategies for the Pine Pitch Canker (PPC) Disease Pathogen Fusarium circinatum in Europe
- 2019
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Ingår i: Forests. - : MDPI AG. - 1999-4907. ; 10
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Forskningsöversikt (refereegranskat)abstract
- Fusarium circinatum Nirenberg & O'Donnel is listed among the species recommended for regulation as quarantine pests in Europe. Over 60 Pinus species are susceptible to the pathogen and it also causes disease on Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) and species in genera such as Picea and Larix. The European Food Safety Authority considers the probability of new introductions-via contaminated seeds, wood material, soil and growing substrates, natural means and human activities-into the EU very likely. Due to early detection, constant surveillance and control measures, F. circinatum outbreaks have officially been eradicated in Italy and France. However, the global spread of F. circinatum suggests that the pathogen will continue to be encountered in new environments in the future. Therefore, continuous surveillance of reproductive material, nurseries and plantations, prompt control measures and realistic contingency plans will be important in Europe and elsewhere to limit disease spread and the "bridgehead effect", where new introductions of a tree pathogen become increasingly likely as new environments are invaded, must be considered. Therefore, survey programs already implemented to limit the spread in Europe and that could be helpful for other EU countries are summarized in this review. These surveys include not only countries where pitch canker is present, such as Portugal and Spain, but also several other EU countries where F. circinatum is not present. Sampling protocols for seeds, seedlings, twigs, branches, shoots, soil samples, spore traps and insects from different studies are collated and compiled in this review. Likewise, methodology for morphological and molecular identification is herein presented. These include conventional PCR with a target-specific region located in the intergenic spacer region, as well as several real-time PCR protocols, with different levels of specificity and sensitivity. Finally, the global situation and future perspectives are addressed.
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| 20. |
- Cleary, Michelle, et al.
(författare)
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Susceptibility of common tree species in Sweden to Phytophthora cactorum, P. cambivora and P. plurivora
- 2017
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Ingår i: Forest Pathology. - : Wiley. - 1437-4781 .- 1439-0329. ; 47
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Tidskriftsartikel (refereegranskat)abstract
- In Sweden, invasive Phytophthora pathogens have been recognized as a growing threat to urban and production forests, calling for an urgent update of regeneration strategies for infested areas. Stem inoculation tests were performed to test the relative susceptibility of common conifer and broadleaved tree species Pinus sylvestris, Picea abies, Larix x eurolepis, Betula pendula, Quercus robur, Fagus sylvatica, Populus trichocarpa and Tilia cordata to the root pathogens Phytophthora cactorum, P. cambivora and P. plurivora commonly isolated from Swedish soils. Results indicate that all the species tested were susceptible and formed lesions following stem inoculation with all three Phytophthora species, but to varying degrees. Of particular interest are the high levels of susceptibility in P. trichocarpa to all three Phytophthora species compared to other tested tree species.
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| 21. |
- Davydenko, Kateryna, et al.
(författare)
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Forewarned is forearmed: harmonized approaches for early detection of potentially invasive pests and pathogens in sentinel plantings
- 2019
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Ingår i: NeoBiota. - : Pensoft Publishers. - 1619-0033 .- 1314-2488. ; , s. 95-123
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Tidskriftsartikel (refereegranskat)abstract
- The number of invasive alien pest and pathogen species affecting ecosystem functioning, human health and economies has increased dramatically over the last decades. Discoveries of invasive pests and pathogens previously unknown to science or with unknown host associations yet damaging on novel hosts highlights the necessity of developing novel tools to predict their appearance in hitherto naive environments. The use of sentinel plant systems is a promising tool to improve the detection of pests and pathogens before introduction and to provide valuable information for the development of preventative measures to minimize economic or environmental impacts. Though sentinel plantings have been established and studied during the last decade, there still remains a great need for guidance on which tools and protocols to put into practice in order to make assessments accurate and reliable. The sampling and diagnostic protocols chosen should enable as much information as possible about potential damaging agents and species identification. Consistency and comparison of results are based on the adoption of common procedures for sampling design and sample processing. In this paper, we suggest harmonized procedures that should be used in sentinel planting surveys for effective sampling and identification of potential pests and pathogens. We also review the benefits and limitations of various diagnostic methods for early detection in sentinel systems, and the feasibility of the results obtained supporting National Plant Protection Organizations in pest and commodity risk analysis.
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| 22. |
- Davydenko, Kateryna, et al.
(författare)
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Fraxinus excelsior seed is not a probable introduction pathway for Hymenoscyphus fraxineus
- 2018
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Ingår i: Forest Pathology. - : Wiley. - 1437-4781 .- 1439-0329. ; 48
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the transmission of Hymenoscyphus fraxineus from infested seed to germinating seedlings of common ash (Fraxinus excelsior) in order to determine the potential risk associated with intra- and intercontinental movement of seed. Neither fungal isolations from necrotic or healthy embryos nor PCR testing with H.fraxineus-specific primers detected the pathogen. Similarly, H.fraxineus was not detected in axenically grown seedlings generated from infested seed lots. The results help clear up prior confusion of the pathogen being seed-borne. Any remaining surface contamination by pathogen spores could be washed off seeds as a quarantine measure.
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| 23. |
- Ghasemkhani, Marjan, et al.
(författare)
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Advanced spectroscopy-based phenotyping offers a potential solution to the ash dieback epidemic
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Natural and urban forests worldwide are increasingly threatened by global change resulting from human-mediated factors, including invasions by lethal exotic pathogens. Ash dieback (ADB), incited by the alien invasive fungus Hymenoscyphus fraxineus, has caused large-scale population decline of European ash (Fraxinus excelsior) across Europe, and is threatening to functionally extirpate this tree species. Genetically controlled host resistance is a key element to ensure European ash survival and to restore this keystone species where it has been decimated. We know that a low proportion of the natural population of European ash expresses heritable, quantitative resistance that is stable across environments. To exploit this resource for breeding and restoration efforts, tools that allow for effective and efficient, rapid identification and deployment of superior genotypes are now sorely needed. Here we show that Fourier-transform infrared (FT-IR) spectroscopy of phenolic extracts from uninfected bark tissue, coupled with a model based on soft independent modelling of class analogy (SIMCA), can robustly discriminate between ADB-resistant and susceptible European ash. The model was validated with populations of European ash grown across six European countries. Our work demonstrates that this approach can efficiently advance the effort to save such fundamental forest resource in Europe and elsewhere.
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| 24. |
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| 25. |
- Grenville-Briggs, Laura J, et al.
(författare)
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Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech (Fagus sylvatica)
- 2017
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Ingår i: Genomics Data. - : Elsevier. - 2213-5960. ; 12, s. 155-156
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Tidskriftsartikel (refereegranskat)abstract
- Phytophthora cactorum is a broad host range phytopathogenic oomycete. P. cactorum strain LV007 was isolated from a diseased European Beech (Fagus sylvatica) in Malmö, Sweden in 2016. The draft genome of P. cactorum strain LV007 is 67.81 Mb. It contains 15,567 contigs and 21,876 predicted protein-coding genes. As reported for other phytopathogenic Phytophthora species, cytoplasmic effector proteins including RxLR and CRN families were identified. The genome sequence has been deposited at DDBJ/ENA/GenBank under the accession NBIJ00000000. The version described in this paper is version NBIJ01000000.
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| 26. |
- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 27. |
- Klein, Alison P., et al.
(författare)
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Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer
- 2018
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- In 2020, 146,063 deaths due to pancreatic cancer are estimated to occur in Europe and the United States combined. To identify common susceptibility alleles, we performed the largest pancreatic cancer GWAS to date, including 9040 patients and 12,496 controls of European ancestry from the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4). Here, we find significant evidence of a novel association at rs78417682 (7p12/TNS3, P = 4.35 x 10(-8)). Replication of 10 promising signals in up to 2737 patients and 4752 controls from the PANcreatic Disease ReseArch (PAN-DoRA) consortium yields new genome-wide significant loci: rs13303010 at 1p36.33 (NOC2L, P = 8.36 x 10(-14)), rs2941471 at 8q21.11 (HNF4G, P = 6.60 x 10(-10)), rs4795218 at 17q12 (HNF1B, P = 1.32 x 10(-8)), and rs1517037 at 18q21.32 (GRP, P = 3.28 x 10(-8)). rs78417682 is not statistically significantly associated with pancreatic cancer in PANDoRA. Expression quantitative trait locus analysis in three independent pancreatic data sets provides molecular support of NOC2L as a pancreatic cancer susceptibility gene.
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| 28. |
- Madigan, Andrew, et al.
(författare)
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Can Hymenoscyphus fraxineus infect hardy members of the Oleaceae other than ash species?
- 2015
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Ingår i: Forest Pathology. - : Wiley. - 1437-4781 .- 1439-0329. ; 45, s. 426-429
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Tidskriftsartikel (refereegranskat)abstract
- The interaction between the ash dieback fungus, Hymenoscyphus fraxineus, and two commonly grown members of the Oleaceae (Forsythiaxintermedia Lynwood' and Ligustrum vulgare) was investigated. Shoots were inoculated with three isolates of H.fraxineus and harvested after 2 and 10weeks. DNA was extracted from tissue collected at the point of inoculation, as well as 15mm below and above (distal), and analysed using fungal-specific ITS primers and specific primers for H.fraxineus. The fungus was frequently detected in tissue at the point of inoculation, but rarely in distal samples. There was no evidence that H.fraxineus was pathogenic on either of the two oleaceous species over the duration of the experiment.
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| 29. |
- Marciulyniene, Diana, et al.
(författare)
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Can pruning help maintain vitality of ash trees affected by ash dieback in urban landscapes?
- 2017
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Ingår i: Urban Forestry & Urban Greening. - : Elsevier BV. - 1618-8667 .- 1610-8167. ; 27, s. 69-75
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Tidskriftsartikel (refereegranskat)abstract
- Hymenoscyphus fraxineus causes a destructive invasive tree disease known as ash dieback threatening the survival of common ash not only in the forests, but also in urban and landscape settings. Pruning is a potential management practice that could help maintain tree vitality and aesthetics in parks, gardens, alleys and recreation areas, as well as maintaining veteran trees having high heritage or cultural value, or trees with high genetic importance (e.g. located in clonal seed orchards). In this study we investigated the maximum distance proximal to the lesion margin at which H. fraxineus can be detected on individual branches infected by the fungus in order to provide recommendations for pruning. Pruning of branches was carried out on 38 trees in southern Sweden. Tissue samples including bark and wood were collected from the margin of the lesion and at 5 cm intervals proximal to the lesion. Molecular analysis revealed presence of H. fraxineus in 91.3% of the investigated lesions. The proportion of lesions at which H. fraxineus could be detected declined with increasing distance from the lesion margin, with a significant reduction in the number of positive samples at 10 cm proximal to the margin. At 30 cm from the lesion edge the pathogen was never detected. Our results suggest that routine pruning may help maintain the vitality of younger trees. Pruning branches at least 35 cm from visible, active lesions in the bark should exclude the fungus and therefore reduce the probability of stem infection by H. fraxineus, however this cultural control tactic may only be economically feasible for high value amenity trees.
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| 30. |
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| 31. |
- Nguyen, Diem, et al.
(författare)
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Foliar fungi of Betula pendula : impact of tree species mixtures and assessment methods
- 2017
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Foliar fungi of silver birch (Betula pendula) in an experimental Finnish forest were investigated across a gradient of tree species richness using molecular high-throughput sequencing and visual macroscopic assessment. We hypothesized that the molecular approach detects more fungal taxa than visual assessment, and that there is a relationship among the most common fungal taxa detected by both techniques. Furthermore, we hypothesized that the fungal community composition, diversity, and distribution patterns are affected by changes in tree diversity. Sequencing revealed greater diversity of fungi on birch leaves than the visual assessment method. One species showed a linear relationship between the methods. Species-specific variation in fungal community composition could be partially explained by tree diversity, though overall fungal diversity was not affected by tree diversity. Analysis of specific fungal taxa indicated tree diversity effects at the local neighbourhood scale, where the proportion of birch among neighbouring trees varied, but not at the plot scale. In conclusion, both methods may be used to determine tree diversity effects on the foliar fungal community. However, high-throughput sequencing provided higher resolution of the fungal community, while the visual macroscopic assessment detected functionally active fungal species.
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| 32. |
- Power, Matthew, et al.
(författare)
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European Fraxinus species Introduced into New Zealand Retain Many of their Native Endophytic Fungi
- 2017
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Ingår i: Baltic Forestry. - 1392-1355. ; 23, s. 74-81
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Tidskriftsartikel (refereegranskat)abstract
- Fraxinus species were introduced in to New Zealand as amenity trees as early as the mid-1850s. As a likely consequence of this early introduction and of their geographic isolation, Fraxinus species in New Zealand have not yet been subjected to the devastating impacts of ash decline caused by Hymenoscyphus fraxinus. This study used isolations, PCR and cloning methods to examine the endophytic fungi associated with Fraxinus excelsior and F. angustifolia on the north island of New Zealand.
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| 33. |
- Skovsgaard, Jens Peter, et al.
(författare)
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Silvicultural strategies for Fraxinus excelsior in response to dieback caused by Hymenoscyphus fraxineus
- 2017
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Ingår i: Forestry. - : Oxford University Press (OUP). - 0015-752X .- 1464-3626. ; 90, s. 455-472
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Forskningsöversikt (refereegranskat)abstract
- Ash dieback caused by the invasive alien fungal pathogen Hymenoscyphus fraxineus often has devastating consequences for the survival, growth and wood quality of Fraxinus excelsior. We analyse the silvicultural implications of ash dieback in forest stands in Europe and review the advice on how to modify management accordingly. We draw on literature as well as unpublished observations and personal experience. The relevant strategy depends on the management objective, the site type (moist or dry), the stand type (pure or mixed stands, even-aged or uneven-aged stands), the age and the degree of dieback. Generally, the strategy should be conservative and trees that are healthy or slightly damaged may be marked and retained. Where dieback is severe, the suggested approach is to harvest remaining commercial timber before value depreciation and to regenerate or replant the area with other tree species. In forests of high value for habitat conservation, it may be advisable to let natural succession proceed unhindered. In all situations, forestry practice plays a key role in implementing in situ and ex situ conservation strategies for ash by preserving trees with low damage levels in all phases of stand development. Wherever there are infected ash trees, risks for operational staff, forest visitors and infrastructure posed by damaged, destabilized ash trees must be minimized.
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| 34. |
- Stenlid, Jan, et al.
(författare)
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Genomes of Hymenoscyphus fraxineus and Hymenoscyphus albida encode surprisingly large cell wall degrading potential, balancing saprotrophic and necrotrophic signatures
- 2017
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Ingår i: Baltic Forestry. - 1392-1355. ; 23, s. 41-51
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Tidskriftsartikel (refereegranskat)abstract
- In Europe, an epidemic is currently occurring on common ash (Fraxinus excelsior). The disease, commonly known as ash dieback, is the result of a biological invasion by the causal Helotialean fungus Hymenoscyphus fraxineus Baral, Queloz, Hosoya. This study describes the genomes of H. fraxineus and H. albidus, a native non-pathogenic sister species to H. fraxineus. The Hymenoscyphus sp. genomes harbour similar and extensive Cell Wall Active Enzyme (CAZYme) repertoires, they appear better at degrading cellulose than e. g. Botrytis but has similar pectin-degrading capacities. In planta, the pathogenic H. fraxineus showed higher gene expression than H. albidus of two of the pectin degrading enzymes, consistent with a higher disruption of primary cell walls and possibly leading to a stronger host reaction. Based on SignalP and Phobious annotations, we identified 2160 and 2006 secreted genes in H. fraxineus and H. albidus, respectively. This is almost twice as many as for most other Helotialean fungi. Two small secreted proteins were transcribed in H. fraxineus, one being a cerato-platinin like protein with a putative role in pathogenicity. No small secreted proteins were detected in the H. albidus transcriptome. It has been suggested that fungal metallopeptidases, can target and degrade non-structural defense proteins in planta. We found that the Hymenoscyphus genomes encode more metallopeptidases than other Helotialean species. In conclusion, the prolonged saprotrophic growth phase on shed ash leaves of H. fraxineus and H. albidus has probably shaped the genomes. Both genomes are highly similar and have CAZYme profiles similar to saprotrophic fungi. The relatively small differences between the two Hymenoscyphus spp. in gene expression are likely indicative of their differential interaction patterns with the host tree F. excelsior.
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| 35. |
- Stephens, Lucas, et al.
(författare)
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Archaeological assessment reveals Earth’s early transformation through land use
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 365:6456, s. 897-902
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Tidskriftsartikel (refereegranskat)abstract
- Humans began to leave lasting impacts on Earth’s surface starting 10,000 to 8000 years ago. Through a synthetic collaboration with archaeologists around the globe, Stephens et al. compiled a comprehensive picture of the trajectory of human land use worldwide during the Holocene (see the Perspective by Roberts). Hunter-gatherers, farmers, and pastoralists transformed the face of Earth earlier and to a greater extent than has been widely appreciated, a transformation that was essentially global by 3000 years before the present.Science, this issue p. 897; see also p. 865Environmentally transformative human use of land accelerated with the emergence of agriculture, but the extent, trajectory, and implications of these early changes are not well understood. An empirical global assessment of land use from 10,000 years before the present (yr B.P.) to 1850 CE reveals a planet largely transformed by hunter-gatherers, farmers, and pastoralists by 3000 years ago, considerably earlier than the dates in the land-use reconstructions commonly used by Earth scientists. Synthesis of knowledge contributed by more than 250 archaeologists highlighted gaps in archaeological expertise and data quality, which peaked for 2000 yr B.P. and in traditionally studied and wealthier regions. Archaeological reconstruction of global land-use history illuminates the deep roots of Earth’s transformation and challenges the emerging Anthropocene paradigm that large-scale anthropogenic global environmental change is mostly a recent phenomenon.
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| 36. |
- Walsh, Naomi, et al.
(författare)
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Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer
- 2019
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press. - 0027-8874 .- 1460-2105. ; 111:6
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Tidskriftsartikel (refereegranskat)abstract
- Background: Genome-wide association studies (GWAS) identify associations of individual single-nucleotide polymorphisms (SNPs) with cancer risk but usually only explain a fraction of the inherited variability. Pathway analysis of genetic variants is a powerful tool to identify networks of susceptibility genes.Methods: We conducted a large agnostic pathway-based meta-analysis of GWAS data using the summary-based adaptive rank truncated product method to identify gene sets and pathways associated with pancreatic ductal adenocarcinoma (PDAC) in 9040 cases and 12 496 controls. We performed expression quantitative trait loci (eQTL) analysis and functional annotation of the top SNPs in genes contributing to the top associated pathways and gene sets. All statistical tests were two-sided.Results: We identified 14 pathways and gene sets associated with PDAC at a false discovery rate of less than 0.05. After Bonferroni correction (P ≤ 1.3 × 10-5), the strongest associations were detected in five pathways and gene sets, including maturity-onset diabetes of the young, regulation of beta-cell development, role of epidermal growth factor (EGF) receptor transactivation by G protein-coupled receptors in cardiac hypertrophy pathways, and the Nikolsky breast cancer chr17q11-q21 amplicon and Pujana ATM Pearson correlation coefficient (PCC) network gene sets. We identified and validated rs876493 and three correlating SNPs (PGAP3) and rs3124737 (CASP7) from the Pujana ATM PCC gene set as eQTLs in two normal derived pancreas tissue datasets.Conclusion: Our agnostic pathway and gene set analysis integrated with functional annotation and eQTL analysis provides insight into genes and pathways that may be biologically relevant for risk of PDAC, including those not previously identified.
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| 37. |
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